I’m not able to reproduce Shield Throw not scaling with damage from its skill tree or your passives. Have you double checked by attacking the Training Dummy in the Council Chambers or End of Time? Try looking at the damage numbers before and after taking a new node (attack a few dozen times, ideally).
If you’re still having issues, please upload a screenshot of your skill tree, passives and items.
I have found that Shield Throw occasionally takes a long time to come off of cooldown during my testing, but I haven’t found the cause yet. If you find out that something makes it happen more consistently, let me know! Thanks.